variant calling

Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types

The paper introduces optimized fluorescence-activated nuclei sorting (FANS) protocols to isolate cell-type-specific nuclei from human and mouse brain tissue for multi-omic analysis.

Patient-Derived Liver Cancer Organoids Reflect Tumor Biology and Their Growth Phenotype Correlates with Clinical Outcomes

Organoids grew from 13 of 27 resected hepatocellular carcinomas. The sequenced lines kept parental mutations, and solid rather than cystic growth marked shorter progression-free survival (HR 13.91).

Analysis of Naturally Arising Simple Deletions in Single Human Colon Crypts with Age

The paper analyzes simple deletions in single human colon crypts across age, finding most are due to strand slippage and NHEJ, with age-related accumulation and radiation effects.

Recent effective population size of the snowy owl (Bubo scandiacus) tracks historical climate variation

This study uses whole-genome resequencing to show that the snowy owl's effective population size has declined over the past 1,600 years, linked to historical climate changes.

Forensic likelihood ratios for shotgun sequencing data from DNA mixtures

The paper develops likelihood ratios for forensic DNA mixtures from shotgun sequencing data, showing they can be unreliable and proposing a combined evidence score to improve accuracy.

A near-ubiquitous plasmid characterises Second Pandemic Yersinia pestis

The paper identifies a plasmid, pTP33, unique to Second Pandemic Yersinia pestis strains, which may have increased transmission and mortality during that pandemic.

Epigenetic maintenance of PRC2-repressed chromatin requires RTT109 but not H3K56 acetylation

The paper identifies RTT109 as essential for maintaining PRC2-repressed chromatin in Neurospora crassa, showing it is required for epigenetic memory but not H3K56 acetylation.

Engineered mRNA-packaging virus-like particles enable efficient and precise mitochondrial base editing in vitro and in vivo

This study develops mtBE-VLPs for transient mitochondrial base editing, achieving high efficiency and reduced off-target effects in vitro and in vivo.

Overcoming a diagnostic blindspot: Identifying balanced translocations in Mendelian rare disease cohorts

This paper develops a specific pipeline to detect balanced reciprocal translocations in genomic data and applies it across multiple cohorts to assess their prevalence and diagnostic impact.

Hidden but Expanding Sampling Bias Distorts Prokaryotic Genome Collections

The paper shows sampling bias in prokaryotic genome collections distorts diversity estimates and proposes a method to detect and reduce this bias.

The limits of Bayesian estimates of divergence times in measurably evolving populations

This paper examines the limits of Bayesian divergence time estimates in microbial evolution, finding that uncertainty scales with distance to calibration points rather than absolute age.

Developmental Convergence Across Diverse Genetic Architectures in Childhood Apraxia of Speech

The paper identifies multiple genetic variants associated with childhood apraxia of speech through whole-exome sequencing and functional analysis, proposing four novel candidate genes.

Distinct sequence grammars of nucleosomal and linker DNA shape mutational and methylation landscapes in cancer

The paper develops DeepND to analyze nucleosomal and linker DNA sequence patterns, identifying motifs linked to cancer mutations and methylation.

Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes

The paper shows that peri/centromeric regions in ape genomes are hypomethylated CpG reservoirs, linking germline hypomethylation to CpG evolution and structural transcriptomic innovation.

The landscape of structural variants in male infertility identified by optical genome mapping

This study identifies structural variants in male infertility using optical genome mapping, finding rare variants in 25% of patients that may contribute to infertility.

Long-read sequencing with targeted assembly of the opsin locus accurately evaluates genes in expressed positions

This paper evaluates long-read sequencing with targeted assembly for accurately analyzing the opsin gene cluster, showing high concordance and improved detection of color vision deficiencies and carrier status.

Comparative functional genomics of six Pectobacterium species reveals core and unique fitness determinants in potato tubers

This study identifies conditionally essential genes in six Pectobacterium species during potato tuber infection, revealing shared and unique fitness determinants.

Monoclonal Antibody Developability from Early Assay Panels: Machine Learning for Formulation and Pharmacokinetic Risk

This paper introduces ACeT, a machine learning framework that predicts formulation and pharmacokinetic risks of monoclonal antibodies using early assay panels, achieving high predictive accuracy and interpretability.

Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus)

This study uses untargeted sequencing to analyze population genetics and pathogen surveillance in timber rattlesnakes, finding genetic distinctness and a color variation locus linked to ALDH4A1.

A 23-copy tandem repeat of a cytochrome P450 gene underlies an adaptive introgression breakthrough in Ciona intestinalis

The paper identifies a 23-copy tandem repeat of the CYP2U1c gene as the structural variant underlying adaptive introgression from C. robusta into C. intestinalis.

Multiple host species maintain genetic diversity in herbivore populations

The paper shows that host diversity maintains genetic diversity in herbivore populations by preserving rare variants and reducing fitness trade-offs.

Long-read PacBio HiFi sequencing resolves the genomic integration site and structure of the Nestin-CreERT2KEisc/J transgene

The paper uses PacBio HiFi sequencing to determine the genomic integration site and structure of the Nestin-CreERT2KEisc/J transgene, revealing deletions and enabling zygosity testing.

X-Y divergence of house fly (Musca domestica) proto-sex chromosomes follows distinct evolutionary trajectories despite residing in the same genome

The paper examines sex chromosome evolution in house flies, finding both canonical and non-canonical divergence patterns despite shared genomic context.

TangentXY: Improved copy-number estimation of sex chromosomes reveals features associated with aneuploidies in chromosomes X and Y across cancers

TangentXY improves copy-number estimation for sex chromosomes, revealing associations between chrX and chrY copy-number alterations and cancer features.

Genome-wide mapping of endogenous topoisomerase cleavage complexes reveals TOP1 at the interface of DNA topological regulation and genome instability

This study introduces pDAIP-seq, a method to map endogenous topoisomerase cleavage complexes, revealing their genomic distribution and role in DNA breaks and genome instability.

LoGicAl: Local ancestry and genotype calling uncertainty-aware ancestry-specific allele frequency estimation from admixed samples

LoGicAl estimates ancestry-specific allele frequencies from admixed samples by accounting for uncertainty in local ancestry and genotype calling, improving accuracy and scalability.

Optical genome mapping identifies source-associated structural variant differences across early-passage human iPSCs

This study uses optical genome mapping to compare structural variant profiles of iPSCs derived from different somatic cell sources, finding differences in SV burden and types between PBMC- and fibroblast-derived clones.

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Extended Tiberius models outscore Helixer and ANNEVO on all 33 genomes from the five clades all three tools cover, and approach BRAKER3 accuracy in four clades without extrinsic evidence.

Branch-Wise Regularization for Heterogeneous GNN-Based MALDI-TOF AMR Prediction with Biomarker-Consensus Edges

This paper evaluates a heterogeneous GNN for AMR prediction from MALDI-TOF spectra, showing it performs better than MLP only at high spectral similarity.

Inferring the landscapes of mutation and recombination in the common marmoset (Callithrix jacchus) in the presence of twinning and hematopoietic chimerism

This study infers mutation and recombination rates in common marmosets, accounting for twinning and chimerism, and identifies PRDM9-mediated recombination hotspots.