Mayar Ali

A deep-learning framework reveals whole-body perturbations at cell level

Doris Kaltenecker, Izabela Horvath, Rami Al-Maskari, Ying Chen et autres

. However, tools for comprehensive, high-resolution analysis of disease-associated changes at the whole-body scale have been lacking. Here we developed MouseMapper, a suite of foundation-model-based deep-learning algorithms enabling multi-system analysis of disease across the entire mouse body. MouseMapper enables whole-body quantitative analysis …

de, ch, us, cn, gb, tr (code pays fourni par la source)

Reversible hypervascularization drives cognitive decline and blood-brain barrier damage during aging

Mihail Ivilinov Todorov, Katalin Völgyi, David‐Paul Minde, Saketh Kapoor et autres

Abstract Cerebrovascular dysfunction emerges early in neurodegeneration, yet how vascular structure, blood–brain barrier (BBB) failure, and cognition are linked remains undefined. Using VesselPro, a whole-brain pipeline integrating perfusion-resolved 3D imaging with spatial proteomics, we mapped vascular aging across the mouse lifespan. We …

de, gb, us (code pays fourni par la source)

DISCO-seq: 3D single-cell transcriptomics of intact biological systems

Harsharan S. Bhatia, Laurent H. A. Simons, Louis Benedikt Kuemmerle, Cristin McCabe et autres

Single-cell transcriptomics has transformed tissue analysis, yet current methods struggle to integrate whole-tissue 3D architecture. Conventional techniques restrict molecular profiling to pre-selected 2D sections, losing systemic context and introducing anatomical bias by sampling less than 0.001% of a whole organism. To overcome …

de, us, gb (code pays fourni par la source)

PEGylation Enhances Colloidal Stability and Promotes Ligand-Mediated Targeting of LAF–Xenopeptide mRNA Complexes

Paul Folda, Eric Weidinger, Johanna Seidl, Mina Yazdi et autres

For complexation of mRNA into polyplexes, double-pH-responsive lipo-xenopeptides (XP), comprising tetraethylene pentamino succinic acid (Stp) and lipoamino fatty acids (LAFs), were combined with PEGylated lipids, either DMG-PEG 2 kDa (DMG-PEG) or azido-group-containing DSPE-PEG 2 kDa (DSPE-PEG-N3), to increase colloidal stability and to …

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Graph neural networks learn emergent tissue properties from spatial molecular profiles

Mayar Ali, Sabrina Richter, Ali Ertürk, David S. Fischer et autres

Tissue phenotypes, such as metabolic states, inflammation, and tumor properties, emerge from both molecular states and spatial cell organization. Spatial molecular assays provide an unbiased view of tissue architecture, enabling phenotype prediction. Graph neural networks (GNNs) offer a natural framework for analyzing …

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LipiGo: A Versatile DNA-Lipid Nanoparticle Hybrid for Precision Drug Delivery

Karoline Kadletz, Ceren Kımna, Valentin Kenneth Reichenbach, Olga Carofiglio et autres

Abstract Lipid nanoparticles (LNPs) are established carriers for nucleic acid delivery, however, achieving efficient delivery to non-hepatic tissues remains a major challenge. Here, we present LipiGo, a nanocarrier platform engineered by integrating short single stranded DNA molecules into the lipid nanoparticle structure. …

de, se (code pays fourni par la source)

Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning

Jie Denny Luo, Müge Molbay, Ying Chen, Izabela Horvath et autres

Abstract Efficient and accurate nanocarrier development for targeted drug delivery is hindered by a lack of methods to analyze its cell-level biodistribution across whole organisms. Here we present Single Cell Precision Nanocarrier Identification (SCP-Nano), an integrated experimental and deep learning pipeline to …

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SELMA3D challenge: Self-supervised learning for 3D light-sheet microscopy image segmentation

Ying Chen, Rami Al-Maskari, Izabela Horvath, Mayar Ali et autres

Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly …

Persistence of spike protein at the skull-meninges-brain axis may contribute to the neurological sequelae of COVID-19

Zhouyi Rong, Hongcheng Mai, Gregor Ebert, Saketh Kapoor et autres

SARS-CoV-2 infection is associated with long-lasting neurological symptoms, although the underlying mechanisms remain unclear. Using optical clearing and imaging, we observed the accumulation of SARS-CoV-2 spike protein in the skull-meninges-brain axis of human COVID-19 patients, persisting long after viral clearance. Further, biomarkers …

de, cn (code pays fourni par la source)

Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity

Doris Kaltenecker, Izabela Horvath, Rami Al-Maskari, Zeynep Ilgin Kolabas et autres

Many diseases, such as obesity, have systemic effects that impact multiple organ systems throughout the body. However, tools for comprehensive, high-resolution analysis of disease-associated changes at the whole-body scale have been lacking. Here, we developed a suite of deep learning-based image analysis …

de, us, gb, ch, tr (code pays fourni par la source)

VIB Hackathon on spatial omics tools and methods

Benjamin Rombaut, Lotte Pollaris, Chananchida Sang-aram, Michiel Ver Cruysse et autres

During a three-day hackathon, work was performed on various topics within the field of spatial omics data analysis. The topics were organized in five workgroups and included benchmarking, pipelines, spatial transcriptomics, spatial proteomics, spatial multi-omics and cell-cell communication. Most tools and methods …

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GraphCompass: spatial metrics for differential analyses of cell organization across conditions

Mayar Ali, Merel Kuijs, Soroor Hediyeh-zadeh, Tim Treis et autres

SUMMARY: Spatial omics technologies are increasingly leveraged to characterize how disease disrupts tissue organization and cellular niches. While multiple methods to analyze spatial variation within a sample have been published, statistical and computational approaches to compare cell spatial organization across samples or …

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