Lukas Valihrach
LightNews LightNews
banner
lukasvalihrach.bsky.social
Lukas Valihrach
@lukasvalihrach.bsky.social
240 followers 530 following 33 posts
Single-Cell & Spatial Transcriptomics | Group Leader at GliaOmics Lab | Head of GeneCore Facility | Co-founder at Carta Genum | Glial Cells in Health & Disease
Posts Replies Media Videos
lukasvalihrach.bsky.social
CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics👍
www.nature.com/articles/s41...
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...
www.nature.com
June 7, 2025 at 5:30 AM
lukasvalihrach.bsky.social
SpotSweeper: spatially aware quality control for 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...
www.nature.com
June 7, 2025 at 5:26 AM
lukasvalihrach.bsky.social
Changing genes, cells and networks to reprogram the brain after stroke🫶
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...
www.nature.com
June 6, 2025 at 10:58 AM
lukasvalihrach.bsky.social
KODAMA enables self-guided weakly supervised learning in spatial transcriptomics
www.biorxiv.org/content/10.1...
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....
www.biorxiv.org
June 4, 2025 at 7:50 AM
lukasvalihrach.bsky.social
A visual–omics foundation model to bridge histopathology with spatial transcriptomics🔥🔥🔥
www.nature.com/articles/s41...
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...
www.nature.com
May 29, 2025 at 6:43 PM
lukasvalihrach.bsky.social
AI-driven 3D Spatial Transcriptomics🤯
arxiv.org/abs/2502.17761
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...
arxiv.org
May 28, 2025 at 7:49 PM
lukasvalihrach.bsky.social
Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies🔥
www.biorxiv.org/content/10.1...
May 28, 2025 at 1:09 PM
lukasvalihrach.bsky.social
How neural stem cell therapy promotes brain repair after stroke🫶
www.cell.com/stem-cell-re...
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...
www.cell.com
May 25, 2025 at 8:57 AM
lukasvalihrach.bsky.social
Cell simulation as cell segmentation⚡
www.nature.com/articles/s41...
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...
www.nature.com
May 25, 2025 at 8:54 AM
lukasvalihrach.bsky.social
Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution🔥
www.cell.com/neuron/abstr...
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...
www.cell.com
May 25, 2025 at 8:50 AM
lukasvalihrach.bsky.social
Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity🙌
www.nature.com/articles/s41...
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...
www.nature.com
May 22, 2025 at 11:35 AM
lukasvalihrach.bsky.social
Beyond cell atlases: spatial biology reveals mechanisms behind disease🫶
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.
www.nature.com
May 21, 2025 at 8:02 PM
lukasvalihrach.bsky.social
CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells🤯
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...
www.nature.com
May 20, 2025 at 6:27 PM
lukasvalihrach.bsky.social
A dynamic and multimodal framework to define microglial states🔥
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.
www.nature.com
May 20, 2025 at 6:13 PM
lukasvalihrach.bsky.social
Cautions on utilizing plasma GFAP level as a biomarker for reactive astrocytes in neurodegenerative diseases
molecularneurodegeneration.biomedcentral.com/articles/10....
Cautions on utilizing plasma GFAP level as a biomarker for reactive astrocytes in neurodegenerative diseases - Molecular Neurodegeneration
molecularneurodegeneration.biomedcentral.com
May 18, 2025 at 5:45 PM
lukasvalihrach.bsky.social
A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity🔥
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
May 16, 2025 at 7:46 PM
lukasvalihrach.bsky.social
Microglia transcriptional states and their functional significance: Context drives diversity🫶
www.cell.com/immunity/ful...
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...
www.cell.com
May 15, 2025 at 7:21 PM
lukasvalihrach.bsky.social
Spatial transcriptomics reveals human cortical layer and area specification🧠
www.nature.com/articles/s41...
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...
www.nature.com
May 15, 2025 at 7:48 AM
lukasvalihrach.bsky.social
Cell-type deconvolution methods for spatial transcriptomics🔥
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,...
www.nature.com
May 14, 2025 at 7:53 PM
lukasvalihrach.bsky.social
Application of spatial transcriptomics across organoids: a high-resolution spatial whole-transcriptome benchmarking dataset
www.biorxiv.org/content/10.1...
May 11, 2025 at 1:47 PM
lukasvalihrach.bsky.social
EnrichSci: Transcript‑guided Targeted Cell Enrichment for Scalable Single‑Cell RNA Sequencing
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...
www.biorxiv.org
May 9, 2025 at 3:15 PM
lukasvalihrach.bsky.social
snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues
www.nature.com/articles/s41...
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...
www.nature.com
May 9, 2025 at 3:14 PM
lukasvalihrach.bsky.social
Next generation statistical framework for next generation spatial transcriptomics data
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
May 9, 2025 at 3:13 PM
lukasvalihrach.bsky.social
A computational framework for mapping isoform landscape and regulatory mechanisms from 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 (...
www.biorxiv.org
May 9, 2025 at 3:11 PM
lukasvalihrach.bsky.social
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...
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...
www.biorxiv.org
May 8, 2025 at 8:11 PM