Lukas Valihrach

CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics - Nature Methods Cell Neural Networks on Spatial Transcriptomics (CellNEST) deciphers patterns of communication between cells in spatially resolved transcriptomics data and can detect both signals between individual c...

CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics👍
www.nature.com/articles/s41...

SpotSweeper: spatially aware quality control for spatial transcriptomics - Nature Methods SpotSweeper is a spatially aware method for quality control of spatially resolved transcriptomics data that corrects for spatial confounding missed by existing methods, including both local and region...

SpotSweeper: spatially aware quality control for spatial transcriptomics👍
www.nature.com/articles/s41...

Changing genes, cells and networks to reprogram the brain after stroke - Nature Neuroscience This review explores how stroke induces changes in gene expression, cell behavior and brain networks, offering insights into recovery. It highlights strategies to enhance cellular reprogramming and br...

Changing genes, cells and networks to reprogram the brain after stroke🫶
www.nature.com/articles/s41...

KODAMA enables self-guided weakly supervised learning in spatial transcriptomics Spatial transcriptomics provides researchers with a powerful tool to investigate gene expression patterns within their native positional context in tissues, revealing intricate cellular relationships....

KODAMA enables self-guided weakly supervised learning in spatial transcriptomics
www.biorxiv.org/content/10.1...

A visual–omics foundation model to bridge histopathology with spatial transcriptomics - Nature Methods OmiCLIP is a visual–omics foundation model that integrates histology and spatial transcriptomics. The associated Loki platform offers accurate and robust tools for alignment, annotation, cell-type dec...

A visual–omics foundation model to bridge histopathology with spatial transcriptomics🔥🔥🔥
www.nature.com/articles/s41...

AI-driven 3D Spatial Transcriptomics A comprehensive three-dimensional (3D) map of tissue architecture and gene expression is crucial for illuminating the complexity and heterogeneity of tissues across diverse biomedical applications. Ho...

AI-driven 3D Spatial Transcriptomics🤯
arxiv.org/abs/2502.17761

Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies🔥
www.biorxiv.org/content/10.1...

How neural stem cell therapy promotes brain repair after stroke In this review, Weber, Rust, and Tackenberg discuss the potential mechanisms by which neural stem/progenitor cell therapy can induce brain recovery after ischemic stroke. They argue that neural stem/p...

How neural stem cell therapy promotes brain repair after stroke🫶
www.cell.com/stem-cell-re...

Cell simulation as cell segmentation - Nature Methods Proseg is a segmentation approach for single-cell spatially resolved transcriptomics data that uses unsupervised probabilistic modeling of the spatial distribution of transcripts to accurately segment...

Cell simulation as cell segmentation⚡
www.nature.com/articles/s41...

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution Xiang et al. generated and demonstrate the utility of a spatiotemporal transcriptomic atlas of intracerebral hemorrhage (ICH) at single-cell resolution across 9 time points between 3 hours and 28 days...

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution🔥
www.cell.com/neuron/abstr...

Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity - Nature Communications Currently, there is an urgent need to evaluate the strengths and limitations of various probe-based full transcriptome methods for formalin-fixed paraffin-embedded tumor tissues. Here, the authors ana...

Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity🙌
www.nature.com/articles/s41...

Beyond cell atlases: spatial biology reveals mechanisms behind disease - Nature Biotechnology As the next generation of spatial transcriptomics tools hits the market, researchers are uncovering previously unknown interactions that could transform clinical research.

Beyond cell atlases: spatial biology reveals mechanisms behind disease🫶
www.nature.com/articles/s41...

CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells - Nature Communications Single-cell sequencing reveals cellular heterogeneity but is challenged by technical noise and batch effects. Here, authors present CellFM, an 800-million-parameter foundation model trained on 100 mil...

CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells🤯
www.nature.com/articles/s41...

A dynamic and multimodal framework to define microglial states - Nature Neuroscience Sankowski and Prinz propose a classification framework for microglia states that considers the contextual plasticity of microglia. Their multimodal classification aligns a robust terminology with biological function and cellular context.

A dynamic and multimodal framework to define microglial states🔥
www.nature.com/articles/s41...

Cautions on utilizing plasma GFAP level as a biomarker for reactive astrocytes in neurodegenerative diseases - Molecular Neurodegeneration

Cautions on utilizing plasma GFAP level as a biomarker for reactive astrocytes in neurodegenerative diseases
molecularneurodegeneration.biomedcentral.com/articles/10....

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories...

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity🔥
www.biorxiv.org/content/10.1...

Microglia transcriptional states and their functional significance: Context drives diversity Single-cell sequencing technologies have revealed the transcriptional diversity of microglia, the brain-resident macrophage population. In this issue, Stevens and colleagues discuss how microglia adap...

Microglia transcriptional states and their functional significance: Context drives diversity🫶
www.cell.com/immunity/ful...

Spatial transcriptomics reveals human cortical layer and area specification - Nature Multiplexed error-robust fluorescence in situ hybridization (MERFISH) together with deep-learning-based nucleus segmentation enabled the construction of a highly detailed and informative spatially res...

Spatial transcriptomics reveals human cortical layer and area specification🧠
www.nature.com/articles/s41...

Cell-type deconvolution methods for spatial transcriptomics - Nature Reviews Genetics Cell-type deconvolution methods are often needed to analyse spatial transcriptomic data to recover cell-type distributions. In this Review, the authors describe the process of cell-type deconvolution,...

Cell-type deconvolution methods for spatial transcriptomics🔥
www.nature.com/articles/s41...

Application of spatial transcriptomics across organoids: a high-resolution spatial whole-transcriptome benchmarking dataset
www.biorxiv.org/content/10.1...

EnrichSci: Transcript‑guided Targeted Cell Enrichment for Scalable Single‑Cell RNA Sequencing Large-scale single‑cell atlas efforts have revealed many aging‑ or disease‑associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular...

EnrichSci: Transcript‑guided Targeted Cell Enrichment for Scalable Single‑Cell RNA Sequencing
www.biorxiv.org/content/10.1...

snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues - Nature Communications Single-nucleus RNA sequencing can be applied to FFPE tissues, but isolating intact nuclei remains challenging. Here the authors develop a low-temperature enzymatic dissociation strategy for rapid, hig...

snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues
www.nature.com/articles/s41...

Next generation statistical framework for next generation spatial transcriptomics data The rapid advancement of spatial transcriptomic technologies, particularly in situ hybridization based methods, has enabled the profiling of gene expression at sub cellular resolution across large tis...

Next generation statistical framework for next generation spatial transcriptomics data
www.biorxiv.org/content/10.1...

A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data Transcript diversity including splicing and alternative 3'end usage is crucial for cellular identity and adaptation, yet its spatial coordination remains poorly understood. Here, we present SPLISOSM (...

A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data 🤔
www.biorxiv.org/content/10.1...

ShinyCell2: An extended library for simple and sharable visualisation of spatial, peak-based and multi-omic single-cell data Single-cell technologies now span multiple modalities, generating large, complex datasets that challenge analysis and sharing. We present ShinyCell2 , an enhanced R package for interactive visualisati...

ShinyCell2: An extended library for simple and sharable visualisation of spatial, peak-based and multi-omic single-cell data
www.biorxiv.org/content/10.1...

Heterogeneity in pericyte inflammatory responses across age and species highlight the importance of human cell models - Molecular Brain Pericytes in the central nervous system are essential for maintaining blood-brain barrier function, regulating blood flow, modulating immune responses, and interacting closely with surrounding cells o...

Heterogeneity in pericyte inflammatory responses across age and species highlight the importance of human cell models
molecularbrain.biomedcentral.com/articles/10....

Redefining CNS immune privilege - Nature Reviews Immunology In this Perspective, Smyth and Kipnis reappraise the concept of immune privilege in the central nervous system. Although immune privilege was originally thought to involve isolation of the central ner...

Redefining CNS immune privilege🫶
www.nature.com/articles/s41...

How the Human Cell Atlas is fast-tracking new medicines Developing new medications can take years. But computational biologist Aviv Regev says AI-powered cell mapping is transforming the process—helping to create life-saving drugs in much less time.

How the Human Cell Atlas is fast-tracking new medicines😍
www.npr.org/2025/04/18/g...

SpatialAgent: An autonomous AI agent for spatial biology Advances in AI are transforming scientific discovery, yet spatial biology, a field that deciphers the molecular organization within tissues, remains constrained by labor-intensive workflows. Here, we ...

SpatialAgent: An autonomous AI agent for spatial biology🤯
www.biorxiv.org/content/10.1...

Chimeric brain models: Unlocking insights into human neural development, aging, diseases, and cell therapies Papetti et al. discuss recent advances in understanding human neural development, aging, and disease uncovered through human-rodent chimeric brain models and examine their potential to drive progress ...

Chimeric brain models: Unlocking insights into human neural development, aging, diseases, and cell therapies
www.cell.com/neuron/abstr...