SIB Swiss Institute of Bioinformatics

A validated amplicon panel for parentage reconstruction and selection monitoring in whitefish (Coregonus spp.)

Abstract Fish populations are notoriously difficult to monitor because their aquatic habitats limit observation. While physical or chemical tagging (e.g., adipose fin removal or Alizarin Red S staining of bones) can reduce growth or survival or requires sacrifice, genetic tools o...

ERGA-BGE reference genome of the bladderpod Alyssoides utriculata (L.) Medik. (Brassicaceae), a yellow-flowering shrub native to Switzerland

We present the chromosome-level genome assembly for bladderrpod, Alyssoides utriculata (Brassicales: Brassicaceae), the only currently accepted species in the genus Alyssoides. The phased assembly comprises two haplotypes with total lengths of 1.01 Gb and 0.98 Gb, respectively. F...

Data-driven identification of small molecules inducing brown adipocyte activation and differentiation

Promoting the recruitment and function of human brown adipose tissue (BAT) holds significant promise for preventing and treating obesity and related metabolic complications. While identifying genes to enhance BAT recruitment and thermogenic activation is crucial, traditional upre...

MOSAIC: Intra-tumoral heterogeneity characterization through large-scale spatial and cell-resolved multi-omics profiling

Understanding the tumor microenvironment has the potential to significantly advance precision oncology, but this effort has been hampered by the scarcity of consistent large data sets. Here, we introduce MOSAIC (Multi-Omics Spatial Atlas in Cancer), a multi-center clinical omics...

BET inhibition induces coordinated repression of the stem cell-related HOX signature in GB uncovering an epigenetic vulnerability

Abstract Background Glioblastoma (GB) is the most aggressive primary brain tumor, characterized by therapy resistance, attributed to a multitude of epi-genetic changes resulting in phenotypic plasticity with altered cell states. To uncover druggable epigenetic vulnerabilities, we...

Large transgene arrays cause aberrant transcription and synthetic molting defects

Abstract Multicopy transgene arrays remain widely used in Caenorhabditis elegans research. It is usually assumed that they behave neutrally, not impacting the phenotype under investigation. Here, we reveal that a previously reported heterochronic extra-molt phenotype associated w...

Autoinducer-2 functions as both a quorum-sensing and metabolic signal in Escherichia coli

ABSTRACT Bacteria integrate diverse environmental signals to coordinate behavior, yet the relationship between nutrient sensing and quorum sensing (QS) remains incompletely understood. Autoinducer-2 (AI-2) is unique among QS signals in that its production is tightly linked to cen...

Alteromonas macleodii breaches the diatom frustule triggering protoplast emergence and programmed necrosis-like death in Thalassiosira rotula

Abstract Diatom-bacteria interactions drive biogeochemical fluxes at the base of the marine food-web. Although bacteria are increasingly recognised as important drivers of algal mortality, the diversity of algicidal strategies remains understudied. Here we show that Alteromonas m...

A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity

Abstract Environmental genomics has transformed our view of the microbial world, yet progress remains largely prokaryote-centric. Among microbial eukaryotes, inconsistent marker choice and limited species-level resolution blunt diversity estimates and hinder cross-study synthesis...

ERGA-BGE Reference Genome: Corema album ((L.) D. Don, 1830) - the Portuguese crowberry, endemic to the Iberian Peninsula.

Corema album is a perennial, dioecious shrub endemic to the Atlantic coast of the Iberian Peninsula and the Azores. It inhabits coastal dune ecosystems from Galicia to the Strait of Gibraltar, where it plays an important ecological role. The goal of this study was to assemble and...

Retinalysis-Vascx: An Explainable Software Toolbox for the Extraction of Retinal Vascular Biomarkers From Color Fundus Images

Purpose: Automatic extraction of retinal vascular biomarkers from color fundus images (CFIs) is crucial for large-scale studies of the retinal vasculature. We present VascX, an open-source software toolbox that extracts biomarkers from CFI artery-vein segmentations. Methods: From...

Epistasis and the changing fitness landscapes of SARS-CoV-2

Abstract Since its emergence in late 2019, millions of SARS-CoV-2 genomes have been generated as part of global efforts to monitor the evolution and spread of the virus. This unprecedented volume of data provides a unique opportunity to study viral evolution at unparalleled resol...

Combining Implementation and Data Sciences to Accelerate Evidence Integration into Healthcare – ImpleMATE

Background The translation of research evidence into routine healthcare practice is often slow and inconsistent, even timely implementation can significantly improve patient outcomes. While implementation science offers strategies to close this gap, current approaches are frequen...

MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography

Abstract Cryo-electron tomography provides unique insights into macromolecular complexes in their native environments, yet membrane analysis remains a major bottleneck due to low signal-to-noise ratios, missing wedge artifacts and the complexity of membrane-associated particles....

The highly heterozygous European amphioxus (Branchiostoma lanceolatum) at the edge of panmixia

Abstract Amphioxus (Cephalochordata) are small marine chordates that have broad ecological ranges, yet as adults form local settlements and exhibit limited mobility. Genomic surveys of two amphioxus species have suggested that they rank among the most genetically diverse metazoan...

Multimodal protective and susceptibility clusters in paediatric atopic dermatitis: A machine learning-based, data-driven observational study

Background Atopic dermatitis (AD) is a chronic inflammatory skin disease that typically develops in early childhood. Differences in AD prevalence and allergy sensitisation patterns have been observed in African populations, including the AmaXhosa population in South Africa, sugge...

SCENE: A Framework for Single-cell Gene Co-expression Network Analysis Across Cell Types and Conditions

Single-cell RNA sequencing (scRNA-seq) enables detailed characterization of gene expression across diverse cell types and conditions. While most analyses focus on differential expression and cell-type abundance, changes in gene–gene interaction patterns—key drivers of cellular fu...

Deep learning aging marker from retinal images unveils sex-specific clinical and genetic signatures

Abstract Retinal fundus images offer a non-invasive window into systemic aging. Here, we fine-tune a foundation model (RETFound) to predict chronological age from color fundus images in 71,343 participants from the UK Biobank, achieving a mean absolute error of 2.85 years. The re...

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcriptomics, delineating higher-order anatomical structures is critical for understand...

Compositional neurosymbolic representations enable efficient active exploration

Abstract Autonomous systems that learn and explore over long horizons face a problem. Standard methods scale poorly in the number of observations, n , precluding sustained operation on bounded hardware. We show that compositional, high-dimensional vector representations inspired...