simulation

Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

mock-fastq-generator: A synthetic FASTQ generator

mock-fastq-generator creates synthetic FASTQ files for testing bioinformatics pipelines without using biological data.

Somatic variant detection using an individual-specific pangenome reference: a case study of a pediatric acute myeloid leukemia patient

This study evaluates the impact of an individual-specific pangenome on somatic variant calling in a pediatric AML patient, finding reduced false positives and altered phylogenetic branching.

Hybrid Drosophila genomes rapidly purge minority ancestry but repeatedly retain selected regions

The paper tracks genome-wide evolutionary dynamics in hybrid Drosophila populations, showing rapid purging of minority ancestry and repeated retention of selected regions through adaptive introgression.

simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants

simSOMA links plant branching topology to meristem cell-lineage dynamics; in simulations, niche size and turnover drive fixation, while terminal organ growth produces most private low-frequency variants.

Goat genome assemblies, nine breeds for pangenome contribution

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

Unexpected excess heterozygosity in a threatened, mycoheterotrophic, self-pollinating orchid

The paper investigates excess heterozygosity in the self-pollinating orchid Corallorhiza bentleyi, finding overdominance likely explains the phenomenon despite selfing and small population size.

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences

SCAR introduces controlled mutations, fragmentation, and damage to sequencing data for benchmarking analyses affected by these factors.

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.

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.

Comparison of the Distribution of Fitness Effects Across Primates

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

Somatic genetic variation shapes clonal selection of memory NK cells

Whole-exome sequencing of memory NK cells from 81 CMV-seropositive donors reveals dominant somatic clones, early-life origin, and positive selection, with Kmt2d loss shifting mouse NK fitness.

Climate-driven niche tracking and genomic resilience shape future distribution of a widespread agricultural weed

The paper examines how blackgrass adapts to climate change by tracking its ecological niche and showing polygenic adaptation, suggesting resilience in agricultural systems.

Revealing the abiotic and biotic drivers of past and future local adaptation in a coastal dogwhelk

The paper identifies abiotic and biotic drivers of local adaptation in dogwhelks and predicts future evolutionary responses to environmental changes.

SketchDNA: A GUI-Enabled Toolkit for Multiscale Modeling of Topological DNA Structures

SketchDNA provides a GUI tool for creating multiscale DNA models, enabling simulations of topological DNA structures and their dynamics.

Minimally invasive monitoring of clonal evolution through integrated single cell and ctDNA analysis

cfClone, a Bayesian model, deconvolves cfDNA whole-genome sequencing using scWGS-derived haplotype-specific clone copy-number profiles to estimate tumour fraction, clonal prevalence, and flag missed clones.

Representation in genetic studies affects inference about genetic architecture

Across UK Biobank, All of Us and FinnGen, the inferred mean direction (sign bias) of rare minor-allele effects varies and is largely explained by each cohort's trait skewness.

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

Sparse or clustered sampling plus rare-variant filtering collapse PCA plots into triangles and three-ray patterns; objective-guided manifold learning on high-dimensional classic PC scores recovers obscured structure.

FORGEPHAST: A fast, haplotype-first complex population and phenotype simulator for biobank-scale simulation

FORGEPHAST simulates large synthetic cohorts with controlled genetic and phenotypic properties, showing polygenic risk score performance varies by phenotype architecture, ancestry, and variant coverage.

Recombination on 'non-recombining' sex chromosomes: empirical insights from the blackspotted stickleback

The paper identifies a recombination event within a non-recombining sex chromosome in blackspotted sticklebacks, challenging the notion that recombination suppression is irreversible.

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

From 338 beetle genomes, eight ancestral linkage groups were inferred; rearrangement rates vary widely, peaking in major radiations, and the X chromosome dates to Holometabola's ancestor.

A theoretical and experimental framework enables low-coverage sequencing for accurate quantification of genome-wide cytosine modification levels

The paper develops and validates Sparse-Seq, a low-coverage sequencing method for accurate quantification of 5mC and 5hmC levels, showing it is more accessible and less variable than mass spectrometry.

Parallel connectivity and genomic divergence but heterogeneous demographic history in sympatric Mediterranean clingfishes

This study examines connectivity and genomic divergence in sympatric Mediterranean clingfishes, finding concordant connectivity patterns but heterogeneous demographic histories.

Comparative pangenomics of Trypanosoma brucei reveal host specialization is driven by targeted or segmental genome streamlining in human and equine-restricted lineages

This paper investigates how Trypanosoma brucei adapts its genome during host specialization, revealing two distinct structural evolution pathways in human and equine-restricted lineages.

Tumour evolution as ground truth for cancer whole-genome sequencing

This paper introduces SCOUT, a synthetic whole-genome sequencing resource for benchmarking cancer genomic analysis, revealing performance issues in complex tumours and highlighting the importance of evolutionary ground truth.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Centromeric origin of megabase-scale Arabidopsis interstitial telomeric repeat domains

The paper identifies centromeres as a source of telomeric sequences in Arabidopsis, showing ITR domains arise from centromeres through amplification and adopt a distinct chromatin state.

Complex Indel Detection: A Simulation-Based Framework and Parsing with FreeBayes

This paper evaluates complex indel detection methods, finding FreeBayes best represents simulated complex indels as single variant records and develops a parsing workflow to extract complex indels from VCF output.

Ancient persistence and recurrent emergence of structural variants across divergent Atlantic salmon lineages

The paper investigates the evolutionary origins of shared structural variants across Atlantic salmon lineages, finding they result from ancient persistence, recurrent mutation, and lineage-specific frequency changes.