variant calling

A stepwise short- and long-read whole genome sequencing strategy resolves previous genetically unresolved inherited retinal disease cases

This paper reanalyzes short-read WGS data and applies long-read WGS to improve genetic diagnosis of inherited retinal disease cases that were previously unresolved.

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

The paper identifies widespread mosaic structural variants in normal human tissues and tumors, with repeat-mediated variants impacting functional elements and enabling noninvasive tumor monitoring through cell-free DNA.

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

The paper analyzes HERV-K(HML-2) structural variation and coding capacity across human pangenomes using long-read sequencing, revealing polymorphic loci and incomplete representation in reference genomes.

Whole-Genome Metagenomics Insights Revealed a Uranium Bio-remediating Cross-Domain Microbiome in the Dhala Impact Structure, India

This study conducts whole-genome metagenomics on uranium-rich soil and water samples from the Dhala impact structure, identifying a unique microbiome with genes for uranium bioremediation.

Non3nExonFinder: transcript-aware identification of shared non-triplet coding exons

Non3nExonFinder identifies shared non-triplet coding exons across transcripts, prioritizing candidates based on CDS status and divisibility by three, with high concordance in validation.

Analyzing Genomic Foundation Models for Viral Sequence Identification

This study evaluates genomic foundation models for viral sequence classification, finding that NTv3-650M achieves high accuracy comparable to BLAST on standard-length sequences.

Nanopore sequencing identifies a new Tyr::CreERT2 allele circulating in existing mouse stocks

The paper identifies a new Tyr::CreERT2 allele in a mouse stock used for melanoma research through nanopore sequencing and confirms its Mendelian inheritance.

kamino: fast proteome-wide variant calling for amino acid phylogenomics

Proteome-wide variant calling builds amino acid phylogenomic alignments orders of magnitude faster than a BUSCO marker pipeline, with similar tree signal in three of four test taxa.

RosaSeed: Faster and Accurate Short Read Alignment Using a Configurable Seeding Strategy

RosaSeed improves short read alignment speed while maintaining accuracy comparable to BWA-MEM2 by using a configurable seeding strategy.

The chromosome level genome of the Blueberry Stem Gall Wasp, Hemadas nubilipennis (Hymenoptera: Ormyridae) on lowbush blueberry (Vaccinium angustifolium) reveals repeat-driven expansion

The paper presents the first chromosome-level genome of the blueberry stem gall wasp, revealing repeat-driven genome expansion and insights into symbiont interactions and host adaptation.

Controlling for DNA dosage with Whole Genome Sequencing improves ATAC-seq peak calling

This paper improves ATAC-seq peak calling by integrating whole-genome sequencing data to control for DNA dosage biases, enhancing peak accuracy and relevance to gene regulation.

Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ

This study introduces HIDEN-SEQ, a transposon-insertion sequencing method for phages, to systematically map gene essentiality and uncover previously unknown viral anti-defense factors.

Development and characterization of a miniaturized focused ultrasound extraction (FUSE) system to enable rapid, point-of-care genetic testing

This paper develops a miniaturized FUSE system for rapid DNA extraction from complex tissues, enabling point-of-care genetic testing.

MMM: A deterministic Mendelian mismatch matrix framework for germplasm collection quality assessment, demonstrated in apple and sweet cherry

MMM assesses germplasm collection quality by quantifying Mendelian mismatches, identifying duplicates, and revealing structural patterns in apple and sweet cherry datasets.

Graph-based pangenome of Venturia inaequalis, the apple scab fungus, reveals structural variants associated with population differentiation

The paper constructs a graph-based pangenome of Venturia inaequalis, identifies structural variants linked to population differentiation, and reveals gene repertoire conservation and virulence-associated diversity.

Somatic mutations and single-nucleus transcriptomics reveal uniquely human properties of neuronal aging

The paper compares somatic mutation rates and transcriptomic changes in neurons across six mammalian species, finding higher mutation accumulation and distinct age-related dysregulation in human neurons.

Inversion characterization in Timema stick insects: from local PCA to pangenome approaches

The paper evaluates methods for detecting and characterizing inversions in Timema stick insects, showing differences in their ability to identify and describe inversion structures.

Efficient primer design for broad-range virus detection: A semi-automated workflow using sequence clustering and varVAMP

This paper presents a semi-automated workflow using sequence clustering and varVAMP to design broad-range RT-qPCR primers for diverse viruses, improving representation and reducing redundancy.

Multimodal single cell analysis reveals a link between flowering and leaf initiation

The paper uses single-cell sequencing to show that Id1 regulates flowering in maize by affecting chromatin remodeling and gene expression, with a genetic interaction between Id1 and Te1 that delays flowering.

Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq

PICARD-seq enables rapid, affordable whole-plasmid sequencing using nanopore technology, improving accuracy and resolving repetitive regions in synthetic constructs.

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

The paper develops crop-specific Nanopore basecalling models for Rosaceae species to improve sequencing quality and enables community use of these models.

ProFinder: Candidate constitutive promoter prediction across the bacterial tree for genetic tool development in non-model species

ProFinder predicts constitutive promoters across bacterial species to aid genetic tool development, achieving high precision and robustness across diverse genomes.

Multi-attribute characterisation of mRNA via MazF endoribonuclease and LC-MS workflows

The paper presents two LC-MS workflows using MazF endoribonuclease to characterise mRNA sequence identity, 5' capping efficiency, and poly(A) tail length and heterogeneity.

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

The paper develops a GT-seq panel to identify species in the Coregonus artedi complex and demonstrates its cross-amplification in related taxa.

CRISPR RNA-Guided Integrase Enables Targeted Genome Engineering and Prophage Functional Genomics in Plant-Pathogenic Pseudomonas

This paper demonstrates CRISPR-INTEGRATE for targeted genome engineering in plant-pathogenic Pseudomonas, enabling gene disruption and prophage excision with phenotypic effects.

The rapid delivery of RNase H variants reveals distinct classes of RNA:DNA hybrids

The paper develops iCoRD to rapidly deliver RNase H1 in live cells and shows it affects specific RNA:DNA hybrids and replication fork stability.

Convergent molecular changes in populations of two pipefish species in the Baltic Sea

This study identifies molecular convergence in Baltic Sea pipefish populations despite differing genomic structures and species relationships.

Isoleucine absence from adult human hemoglobin is mirrored in mosquito proteomes and limits malaria parasite growth

The paper shows that isoleucine deficiency in human hemoglobin mirrors mosquito proteomes and limits malaria parasite growth.

Using population-level whole-genome sequencing to profile colistin resistance evolution dynamics in diverse clinical Pseudomonas aeruginosa lineages

The paper uses population-level whole-genome sequencing to study colistin resistance evolution in diverse Pseudomonas aeruginosa lineages under increasing colistin pressure.

FourC: identifying significant and differential contacts in 1D chromatin conformation data

FourC identifies significant and differential contacts in 4C-seq data using a Bayesian model and Gaussian processes to address duplication and model spatial patterns.