Ian Ferenc Diks

Multimodal brain cell atlas across the adult macaque lifespan

Xiao Zhang, Guangyao Lai, Xiangyu Guo, Wen Ma et autres

cn, me, mo, sa, es, it, de, se, th, gb, hk (code pays fourni par la source)

MCPmed: a call for Model Context Protocol-enabled bioinformatics web services for LLM-driven discovery

Matthias Flotho, Ian Ferenc Diks, Philipp Flotho, Leidy-Alejandra G Molano et autres

Bioinformatics web servers are critical resources in modern biomedical research, facilitating interactive exploration of datasets through custom-built interfaces with rich visualization capabilities. However, this mostly human-centric design limits machine readability for large language models (LLMs) and deep research agents. We address this …

de (code pays fourni par la source)

PBMCpedia: a harmonized PBMC scRNA-seq database with unified mapping and enhanced celltype annotation

Erich Hoffmann, Lara Hombrecher, Ian Ferenc Diks, Matthias Flotho et autres

Single-cell transcriptomic studies of peripheral blood mononuclear cells (PBMCs) offer valuable insights into immune states across diverse biological conditions, yet cross-study integration remains difficult due to divergent preprocessing and annotations. PBMCpedia addresses this by uniformly reprocessing 519 samples (over 4.3 million cells) …

de (code pays fourni par la source)

Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer’s disease

Matthias Flotho, Andrew C. Yang, Fabian Kern, Simon Graf et autres

ABSTRACT The neurovascular unit is critical for brain health, and its dysfunction has been linked to Alzheimer’s disease (AD). However, a cell-type-resolved understanding of how diverse vascular cells become dysfunctional and contribute to disease has been missing. Here, we applied Vessel Isolation …

de, us (code pays fourni par la source)

ROSMAP-Compass: A data-harmonised, AI-ready atlas of 22 million single nuclei from the ROSMAP cohort

Matthias Flotho, Ian Ferenc Diks, Philipp Flotho, Pascal Hirsch et autres

The Religious Orders Study and Memory and Aging Project (ROSMAP) cohort has generated the world's most comprehensive single-cell transcriptomic resource for Alzheimer's disease research. Naturally, in a project spanning multiple years with dozens of research groups involved, the resulting data landscape shows …

de, us (code pays fourni par la source)

PBMCpedia: A Harmonized PBMC scRNA-seq Database With Unified Mapping and Enhanced Celltype Annotation

Erich Hoffmann, Lara Hombrecher, Ian Ferenc Diks, Matthias Flotho et autres

Reproducibility in single-cell transcriptomics remains limited by inconsistent preprocessing, heterogeneous cell type annotations, and study-specific batch effects. This challenge is particularly pronounced in peripheral blood mononuclear cell (PBMC) datasets, which are central to immunological research but rarely harmonized across studies. We present …

de (code pays fourni par la source)

SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale

Ian Ferenc Diks, Matthias Flotho, Andreas Keller

Abstract Single-cell RNA sequencing studies increasingly generate datasets exceeding 10 million cells, surpassing the memory capacity of standard analytical tools on typical institutional infrastructure. Here we introduce SingleRust, a computational framework that addresses these constraints through systematic algorithmic optimizations and systems-level design. …

de (code pays fourni par la source)

Single-cell Spatial Transcriptomics Reveals Disease-specific Microenvironmental Niches in Neurodegeneration and COVID-19

Simon Graf, Nicole Ludwig, Matthias Flotho, Annika Engel et autres

ABSTRACT Neurodegenerative diseases and infections can produce lasting effects on brain function, yet the spatial molecular mechanisms underlying these changes remain poorly understood. Here, we present high-resolution spatial transcriptomics of 40 postmortem brain samples from patients with Parkinson’s disease, frontotemporal dementia, dementia …

cn, de, us, Botswana (code pays fourni par la source)

Multimodal brain cell atlas across the adult macaque lifespan

Xiao Zhang, Guangyao Lai, Xiangyu Guo, Wen Ma et autres

SUMMARY High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including …

cn, th, mo, hk, it, de, ca, se, gb, pt, my (code pays fourni par la source)