We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibi

A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is yet to be defined. In this study, we manually curated 1235 SVs which can ultimately be used to evaluate SV callers ortrain machine learning models. We devel

Maternal vaccination, resulting in transfer of protective IgG across the placenta, represents a promising strategy to prevent neonatal disease caused by group B Streptococcus (GBS). The prototype vaccine GBS-NN, a fusion protein consisting of the N-terminal domains of the alpha-like protein (Alp) family members AlphaC and Rib, has been shown to display a good safety profile and to elicit a strong

The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Techno

Light field microscopy (LFM) has emerged as a powerful tool for fast volumetric image acquisition in biology, but its effective throughput and widespread use has been hampered by a computationally demanding and artefact-prone image reconstruction process. Here, we present a novel framework consisting of a hybrid light-field light-sheet microscope and deep learning-based volume reconstruction, wher

Understanding how hematopoietic stem and progenitor cells (HSPCs) are regulated is of central importance for the development of new therapies for blood disorders and stem cell transplantation. To date, HSPC regulation has been extensively studied in vitro and in animal models, but less is known about the mechanisms in vivo in humans. Here, in a genome-wide association study on 13,167 individuals,

BACKGROUND: From the beginning of COVID-19 pandemic, pregnant women have been considered at greater risk of severe morbidity and mortality. However, data on hospitalized pregnant women show that the symptom profile and risk factors for severe disease are similar to those among women who are not pregnant, although preterm birth, Cesarean delivery, and stillbirth may be more frequent and vertical tr

Incidence of differentiated thyroid carcinoma (DTC) varies considerably between ethnic groups, with particularly high incidence rates in Pacific Islanders. Here, we conducted a genome-wide association study (GWAS) involving 1,554 cases/1,973 controls of European ancestry and 301 cases/348 controls of Oceanian ancestry from the EPITHYR consortium. Our results confirmed the association with the know

We performed the largest genome-wide meta-analysis (GWAMA) (Max N=26,494) of the levels of 184 cardiovascular-related plasma protein levels to date and reported 592 independent loci (pQTL) associated with the level of at least one protein (1308 significant associations, median 6 per protein). We estimated that only between 8-37% of testable pQTL overlap with established expression quantitative tra

Severe COVID-19 is characterised by immunopathology and epithelial injury. Proteomic studies have identified circulating proteins that are biomarkers of severe COVID-19, but cannot distinguish correlation from causation. To address this, we performed Mendelian randomisation (MR) to identify proteins that mediate severe COVID-19. Using protein quantitative trait loci (pQTL) data from the SCALLOP co

Background Vaccine effectiveness against COVID-19 needs to be assessed in diverse real-world population settings.Methods A cohort study of 805 741 residents in Skåne county, Southern Sweden, aged 18-64 years, of whom 26 587 received at least one dose of the BNT162b2 vaccine. Incidence rates of COVID-19 were estimated in sex- and age-adjusted analysis and stratified in two-week periods with substan

The overall aim of this PhD thesis was to investigate sedimentary micro-environments and ecosystemfunctioning of two coastal areas. We combined different high spatial resolution methods and multivariate analyses atdifferent spatio-temporal scales to reveal interactions between benthic faunal and geochemical compartments. Firstly,we investigated two stations with contrasted oxygen, nitrate and mang

Aim: Health and nutrition in early childhood are essential for survival, growth and adult life outcomes. As such, a number of global and national interventions have been pursued to improve early childhood health and nutrition. However, child malnutrition is pervasive and endemic across the sub Saharan Africa. This paper therefore assesses the nature and trends of socioeconomic inequalities in chil

Improving household access and use of clean energy has been central to global development efforts in recent years. The negative effects of energy poverty on health, climate, livelihoods and economy has led to increased investments towards achieving universal access to clean energy. However, significant deprivations in clean energy remains, especially in developing countries. Energy poverty may inv

Purpose: This study aims to estimate the degree and nature of socioeconomic-related inequalities in sexual and reproductive health in Ghana and further assesses causes of these inequalities using decomposition technique. The authors assess the contribution of personal characteristics of the woman including access to health information and health seeking behaviours, household and locational charact

Purpose: The purpose of this paper is to assess the trends of socioeconomic-related inequalities in maternal healthcare utilization in Ghana between 2003 and 2014 and examine the causes of inequalities in maternal healthcare utilization in Ghana. Design/methodology/approach: Data are drawn from three rounds of the Ghana Demographic and Health Survey collected in 2003, 2008 and 2014, respectively.

Ghana has witnessed tremendous economic growth since the 1990s and attained the Millennium Development Goals target of halving poverty. This notwithstanding, inequality in Ghana increased over the same period, suggesting growth benefits were not equitably distributed. This study provides evidence on the determinants of household consumption expenditure and factors that explain rural-urban welfare