Biology subjects

Pala, M.

Publications and source records attributed to Pala, M..

4 recordsLinked to original sources

bioRxiv2026

COLSTATS: an interactive web platform for systematic colocalization of GWAS and QTL summary statistics

Colocalization of GWAS with QTL data is pivotal for identifying shared genetic determinants of molecular traits and diseases yet remains hindered by fragmented data sources and technical barriers. COLSTATS addresses this gap by offering a web-based Shiny platform that integrates 1,648,851 harmonized summary statistic datasets from key resources (GWAS Catalog, UK Biobank, GTEx, BluePrint, eQTLGen, and immune-phenotype studies), all formatted as VCFs aligned to hg38 with uniform chr_pos_ref_alt variant identifiers. Users can interactively select two traits, specify a genomic region or gene, define priors, and execute colocalization via coloc.abf, with results displayed in tabular and graphical form, downloadable as PDF, CSV, or PNG. The system includes result caching, history tracking, and an intuitive interface for streamlined exploration.COLSTATS is freely accessible at https://colstats.irgb.cnr.it. This resource empowers researchers, including non-bioinformaticians, to perform transparent and reproducible colocalization analyses efficiently.

bioinformatics↗

bioRxiv2025

Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups

The first phase of the ancient DNA revolution painted a broad-brush picture of European Holocene prehistory, whereby 6500-4000 BCE, farmers descending from western Anatolians mixed with local hunter-gatherers resulting in 70-100% ancestry turnover, then 3000-2500 BCE people associated with the Corded Ware complex spread steppe ancestry into north-central Europe. We document an exception to this pattern in the wider Rhine-Meuse area in communities in the wetlands, riverine areas, and coastal areas of the western and central Netherlands, Belgium and western Germany, where we assembled genome-wide data for 109 people 8500-1700 BCE. Here, a distinctive population with high hunter-gatherer ancestry ([~]50%) persisted up to three thousand years later than in continental European regions, reflecting limited incorporation of females of Early European Farmer ancestry into local communities. In the western Netherlands, the arrival of the Corded Ware complex was also exceptional: lowland individuals from settlements adopting Corded Ware pottery had hardly any steppe ancestry, despite a characteristic early Corded Ware Y-chromosome. The limited influx may reflect the unique ecology of the regions river-dominated landscapes, which were not amenable to wholesale adoption of the early Neolithic type of farming introduced by Linearbandkeramik, making it possible for previously established groups to thrive, and creating a persistent but permeable boundary that allowed transfer of ideas and low-level gene flow. This changed with the formation-through-mixture of Bell Beaker using populations [~]2500 BCE by fusion of local Rhine-Meuse people (9-17%) and Corded Ware associated migrants of both sexes. Their expansion from the Rhine-Meuse region then had a disruptive impact across a much wider part of northwest Europe, including Britain where its arrival was the main source of a 90-100% replacement of local Neolithic peoples.

genomics↗

bioRxiv2024

Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa

BackgroundThe Islamic influence on the Iberian Peninsula left an enduring legacy culturally and linguistically, however the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late Medieval period through ancient DNA. ResultsOur comprehensive genomic analysis uncovered gene flow from various Mediterranean regions into Iberia before the Islamic period, supporting a pre-existing pan-Mediterranean homogenization phenomenon during the Roman Empire. North African ancestry is present but sporadic in late antiquity genomes but becomes consolidated during the Islamic period. We uncovered one of the earliest dated Islamic burials in Spain, which showed high levels of inbreeding. For the first time we also prove the persistence of North African ancestry in a Christian cemetery until the 17th century, in addition to evidence of slave traffick from the Maghreb. ConclusionsThis study reveals the complex interaction between political events and cultural shifts that influenced the population of eastern Iberia. It highlights the existence of a slave trade and underscores the lasting impact of historical events, such as the Expulsion of the Moriscos in 1609 CE, on the regions genetic and cultural landscape through mass population displacement and replacement.

evolutionary biology↗

bioRxiv2019

Genetic dysregulation of gene expression and splicing during a ten-year period of human aging

Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age. We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age; 93% of samples cluster with their own measurement at another age, and there is a strong correlation of genetic effects on expression between the two ages (median{rho} G = 0.96). Despite this, we identify 1,291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories of aging. Further, 7.8% and 9.6% of tested genes show a reduction in genetic associations with expression and alternative splicing in older age, with impacted genes enriched in DNA repair pathways. Together these findings indicate that, although gene expression and alternative splicing and their genetic regulation are mostly stable late in life, a small subset of genes is dynamic and is characterized by changes in expression and splicing and a reduction in genetic regulation.

genomics↗