Heterozygous gain-of-function (GOF) mutations in signal transducer and activator of transcription 1 (STAT1) cause an inborn error of immunity characterized by immune dysregulation, recurrent infections and various autoimmune manifestations. However, the precise pathogenic mechanism by which STAT1 GOF contributes to autoimmunity remains elusive. In our cohort, STAT1-GOF patients exhibit biased circulating follicular helper T (cTfh) […]
The BRCA1-A complex restricts replication fork reversal-dependent DNA repair in ATM deficient cells
Ataxia Telangiectasia Mutated (ATM) kinase deficiency results in cancer susceptibility and drug sensitivity. Deficiency in either the BRCA1 interacting A complex or XRCC4/Ligase 4 confers resistance to Topoisomerase I or PARP1 inhibitors in ATM-deficient cells. This suggests that BRCA1-A directs toxicity to fork-damaging agents in ATM mutated cells vis-a-vis illegitimate end-joining. Here, we show that […]
A comparative analysis of fruit feeding among Mediterranean passerine birds
We analyse fruit feeding ecology of Mediterranean passerines in a regional, trait-based framework, with emphasis on their role as seed dispersers in Iberian scrub and woodland habitats. We compiled ecomorphological traits for 146 species (N> 6000 individuals), including body mass, gape width, and gut morphology and transit rates, from mist-netted birds, museum specimens, and published […]
Evolutionary and functional genomics reveal that Ralstonia wilt pathogens actively deploy antimicrobial warfare while leveraging physiological adaptations during plant infection
The xylem pathogens in the Ralstonia solanacearum species complex (RSSC) cause wilt diseases that threaten global food security. These diverse pathogens are highly adapted to the in planta environment where they proliferate and cause rapid, aggressive diseases. To understand the genetic underpinnings of these pathogens’ in planta fitness, we performed forward genetic screens in three […]
Dissociable contributions of cortical thickness and surface area to cognitive ageing: evidence from multiple longitudinal cohorts.
Cortical volume, a widely-used marker of brain ageing, is the product of two genetically and developmentally dissociable morphometric features: thickness and area. However, it remains unclear whether these two features have dissociable consequences for cognitive ageing. To address this, we analyse cross-sectional and longitudinal neuroimaging and cognitive data from one discovery cohort (Cam-CAN) and two […]
Animal collocation revisited: intercohort comparison and a case study comparing call combinations between sexes in common marmosets
Many animals communicate using sequences of signals, but identifying recurrent, non-random signal combinations remains methodologically challenging. Collocation analyses are increasingly popular approaches for detecting which signals animals combine at rates greater than expected by chance. However, existing methods for animal collocation analysis face several limitations that reduce their statistical rigour: they lack uncertainty estimates, fail […]
Helicase: Vectorized parsing and bitpacking of genomic sequences
Modern sequencing pipelines routinely produce billions of reads, yet the dominant storage formats (FASTQ and FASTA) are text-based and sequential, making high-throughput parsing a persistent bottleneck in bioinformatics. Their regular, line-oriented structure makes them well-suited to SIMD vectorization, but existing libraries do not fully exploit it. We present vectorized algorithms for high-throughput FASTA/Q parsing, with […]
Ineffectual Genomic Error Correction Under Environmental Perturbation Dynamically Regulates Mutational Supply and Robustness
Adaptive evolution depends on the supply of heritable variation, yet excessive mutation threatens viability by degrading essential molecular functions. Here, we show that this trade-off emerges naturally from the kinetic proofreading mechanism that controls replication fidelity. In our model, environmental shifts alter the optimal driving rate constant of proofreading enzymes, transiently elevating replication error rates […]
aaKomp: Alignment-free amino acid k-mer matching for genome completeness assessment at scale
In de novo sequencing projects, genome assembly optimization requires evaluating a number of candidate assemblies to identify optimal tool parameters. Yet, current completeness assessment tools like BUSCO and compleasm require 10-80 minutes per evaluation for gigabase-scale genomes, transforming what should be rapid iteration into time-intensive processes. These tools rely on alignment-based approaches and fixed ortholog […]
DNA Traces on the Shroud of Turin: Metagenomics of the 1978 Official Sample Collection
This research provides original insights into the diversity of DNA extracted from samples collected in 1978 from the Turin Shroud, revealing its biological complexity through rigorous DNA and metagenomic analyses. Our findings highlight its preservation conditions and environmental interactions, offering valuable perspectives into the identified genetic variants, which originated from multiple biological sources. Several human […]
ATHILAfinder: a tool to detect ATHILA LTR retrotransposons in plant genomes
Motivation The ATHILA lineage of LTR retrotransposons has colonised all branches of the plant tree of life. In Arabidopsis thaliana and A. lyrata, ATHILA elements have invaded centromeres, influencing the genetic and epigenetic organisation, and driving satellite evolution. To assess the broader significance of ATHILA across plants, a computational pipeline is needed to identify ATHILA […]
Microfluidic low-input profiling reveals lncRNA roles in disease
Long noncoding RNAs (lncRNAs) regulate gene expression through binding to DNA, various RNAs, and proteins, playing potentially important but poorly understood roles in diseases. Existing approaches for profiling lncRNA-chromatin interactions at the genome scale require large quantities of input material (e.g., 100 million cells per assay). Applying these technologies to tissue samples has been challenging […]