variant calling

pTRIP, a novel integration plasmid for Listeria monocytogenes

The paper introduces pTRIP, a new integrative plasmid for Listeria monocytogenes that allows stable gene integration without antibiotic selection.

Assessing Hardy-Weinberg Equilibrium in T2T-aligned 1000 Genomes Project

The paper assesses Hardy-Weinberg equilibrium deviations in whole genome sequence data from the 1000 Genomes Project, identifying SNPs with technical rather than biological deviations.

An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes

DAIseg is a new HMM-based method that detects both Neanderthal and Denisovan introgression in modern human genomes without archaic references, outperforming existing methods in Papuan populations.

Genome-wide structural variant landscape following HDR-enhanced CRISPR editing in human hematopoietic stem and progenitor cells

The paper investigates structural variant induction in human hematopoietic stem and progenitor cells during HDR-enhanced CRISPR editing, finding that SVs occur even without DNA-PK inhibitors and increase with multiple edits.

A Scalable Distributed-Memory MPI Implementation of Smith-Waterman with Token-Passing Traceback

This paper presents a distributed-memory MPI implementation of the Smith-Waterman algorithm with token-passing traceback, enabling scalable and memory-efficient sequence alignment on large datasets.

Benchmarking CUT&RUN analysis using motif enrichment

This study benchmarks CUT&RUN peak callers using motif enrichment, finding that MACS2 outperforms SEACR in most scenarios with optimal preprocessing.

Telomere length of both parents contributes to heritable POT1 cancer-predisposition syndrome

The paper investigates how POT1 mutations affect telomere inheritance and cancer risk by analyzing telomere length in families with POT1 mutations.

Estimating de novo mutation rates using parent-offspring pairs

OOPS estimates de novo mutation rates using single parent-offspring pairs, achieving comparable accuracy to trio-based methods.

NanoDel: Identification of large-scale mitochondrial DNA deletions using long-read sequencing

NanoDel detects large-scale mitochondrial DNA deletions using long-read sequencing, showing improved sensitivity and accuracy over existing methods.

Ancestree: unified likelihood inference of ancestral alleles under supplied or inferred genealogies

Ancestree infers ancestral alleles using genealogies, supporting various inputs and providing posterior probabilities, with improved accuracy over fixed-tree methods.

Advancing Neurological Liquid Biopsy via Six-Base Sequencing of Cerebrospinal Fluid Cell-Free DNA

This paper uses 6-base sequencing to analyze DNA modifications in cerebrospinal fluid cell-free DNA, providing insights into neurodegenerative biology for liquid biopsy applications.

Modified crRNA variants for precise targeting of point mutations in human mitochondrial DNA by CRISPR-Cas12a

This study identifies modified crRNA variants for precise targeting of point mutations in human mitochondrial DNA using CRISPR-Cas12a, showing effective discrimination and base editing in vitro and in human cells.

Isocall enables scalable transcript identification from long-read RNA-sequencing data

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

Genomic evidence for Z-W differentiation in Pacific saury (Cololabis saira) and sex-chromosome diversity in Beloniformes

The paper confirms a ZZ/ZW sex-determination system in Pacific saury using ddRAD-seq and Pool-seq, identifies a female-specific marker, and highlights sex-chromosome diversity in Beloniformes.

pydreg: a fast Python package for identifying active cis-regulatory elements from nascent transcription

pydreg is a Python port of dREG that improves runtime and memory efficiency while maintaining similar performance in identifying active cis-regulatory elements.

Quantitative and sensitive neuroblastoma minimal residual disease detection using extrachromosomal DNA (ecDNA) breakpoints

This study develops a method to detect minimal residual disease in neuroblastoma using ecDNA breakpoints, achieving high sensitivity and specificity in bone marrow samples.

DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens

DNAharvester is a Nextflow pipeline designed to process highly degraded DNA from ancient specimens, improving authentic data recovery through modular workflows and contamination mitigation.

Genomic Insights into Multi-Drug-Resistant, Klebsiella pneumoniae Isolated from an Infertile Woman: A Comprehensive Analysis of Antibiotic Resistance and Virulence Factors

This study analyzes the genome of a multidrug-resistant Klebsiella pneumoniae strain to identify resistance mechanisms and virulence factors.

Temperature-Switchable Genome Editors from Extremophile-Derived Integrases

The paper identifies temperature-responsive integrases from extremophiles and demonstrates their use in creating temperature-switchable genome editing systems.

Using Mapping-Profiles to Refine Strain-Level Metagenomic Classification

StrainRefine improves strain-level metagenomic classification by refining read mappings using profile similarity, reducing false positives while maintaining accuracy.

The hidden diversity: Replication-strand asymmetry shapes short-term nucleotide and structural variation in an RNA virus

The paper characterizes replication dynamics and short-term evolutionary patterns of OrV, revealing strand asymmetry, mutational filtering, and non-standard genomes.

Scalable Assembly of Ascaris Mitogenomes from Whole-Genome Data Reveals a Novel Clade

The paper presents a bioinformatic pipeline for assembling Ascaris mtDNA from low-coverage whole-genome data, revealing a novel clade (Clade D) in human samples from Ethiopia.

H-NS silences antiviral immunity through 3D chromatin compaction

This study shows H-NS silences bacterial antiviral immunity by compacting chromatin, and its deletion enhances phage defense in E. coli.

Transposable element activity and polymorphisms drive structural variability within and between individual in bivalves

This study identifies structural variants and transposable element insertions in oysters, showing their role in genomic diversity and adaptation to environmental conditions.

A native single-transcript TnpB architecture enables efficient virus-induced genome editing and visual screening of heritable progeny harboring phenotypically silent edits

This paper describes a compact TnpB system for virus-induced genome editing in plants, enabling efficient editing and visual screening of heritable progeny.

A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation

This paper benchmarks how reference genome choice affects human genome interpretation by comparing T2T references and finding ancestry-matched references provide more accurate variant discovery.

A simple and accurate method for inferring missing ploidy information from sequence data

This paper introduces a machine learning method to infer ploidy from sequencing data, achieving high accuracy on simulated and empirical datasets.

Bacterial DNA methylation amplifies the shared A-to-G and G-to-A substitution bias in nanopore sequencing

The paper identifies a shared A-to-G and G-to-A substitution bias in nanopore sequencing, amplified by bacterial DNA methylation, and shows this bias is concentrated around methylation motifs.

Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows

Pioneer and Altimeter provide fast, accurate analysis of DIA proteomics data, improving peptide coverage and speed compared to existing tools.

'PePApipe': a complete bioinformatics analysis pipeline for African Swine Fever Virus genome

PePApipe is a bioinformatics pipeline for ASFV genome analysis that integrates multiple tools into an automated workflow, enabling rapid and reproducible genomic analysis with minimal bioinformatics expertise.