Nikolaus Rajewsky

Integrating UHPLC-MS and MALDI-MSI for Spatial Nucleoside Profiling in FFPE Breast Cancer: A Multimodal Molecular Pathology Framework

This paper develops a workflow integrating UHPLC-MS and MALDI-MSI to spatially map nucleosides in FFPE breast cancer tissues, revealing metabolic changes across tumor stages and validating findings in patient samples.

Tau spreading coordinates intercellular lipid flux enhancing neuronal resilience to lipid toxicity

This study shows that spreading tau coordinates lipid homeostasis by promoting neuronal lipid efflux and enhancing resilience to lipid toxicity.

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

The paper introduces circVDJ-seq for efficient T cell receptor profiling from single-cell and spatial multi-omics data, revealing distinct immune microenvironments and T cell clonality patterns in various clinical contexts.

Epithelial mesenchymal transition initiates precancer states in BRCA1 mutation carriers

The paper shows that EMT in BRCA1 carriers leads to precancerous states through morphological, transcriptomic, and functional changes.

pyTrance finds co-localizing RNAs in subcellular spatial transcriptomics data

pyTrance identifies co-localizing RNAs in spatial transcriptomics data with higher accuracy than existing methods, revealing biologically relevant RNA co-localization patterns in mouse brain tissue.

InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics

InterScale models both local and global cellular interactions in spatial transcriptomics data, revealing spatially restricted differentiation programs and disease-associated tissue remodeling.

MicroRNAs are required within a critical time window to define neural patterning during early human brain development

The paper shows miRNAs are essential during a specific time window for proper neural patterning in human brain development, with disruption causing defects in forebrain identity.

Lineage origin and developmental context shape tumor states in MYCN-dependent zebrafish neuroblastoma

This study shows lineage history and developmental context jointly shape tumor-state architecture in MYCN-driven zebrafish neuroblastoma.

Spatiotemporal dynamics of tumor microenvironment remodelling

This study uses spatial transcriptomics to analyze tumor microenvironment remodeling dynamics in triple-negative breast cancer, identifying early stromal programs as potential therapeutic targets.

OpenDVP: An experimental and computational framework for community-empowered deep visual proteomics

The paper introduces openDVP, a framework for deep visual proteomics, demonstrating its application in three tissue studies to integrate spatial single-cell phenotypes with proteomic data.

Scalable image-based visualization and alignment of spatial transcriptomics datasets

The paper introduces STIM, a framework for visualizing and aligning spatial transcriptomics data, demonstrating its use on mouse and human tissue samples.

UBE3C links ubiquitin signaling to epitranscriptomic control of cortical neurogenesis

The paper shows UBE3C regulates cortical neurogenesis and glial fate through m6A methylation, with mutations disrupting this process and offering therapeutic targets.

Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure

This study shows that mutant Huntingtin causes neurodevelopmental issues in human brain organoids by disrupting CHCHD2, leading to mitochondrial and metabolic problems.

Deep learning-driven neuromorphogenesis screenings identify repurposable drugs for mitochondrial disease

The paper identifies repurposable drugs for mitochondrial disease by using deep learning to screen for compounds that improve neuronal commitment and neurogenesis in Leigh syndrome organoids.

Open-ST: High-resolution spatial transcriptomics in 3D

Open-ST provides a high-resolution, 3D spatial transcriptomics method to study tissue molecular organization, revealing spatially contiguous structures and biomarkers in tumors and lymph nodes.

ciRS-7 and miR7 regulate ischemia induced neuronal death via glutamatergic signaling

The paper shows that ciRS-7 and miR-7 regulate ischemia-induced neuronal death through glutamatergic signaling in mice.

Prox2+ and Runx3+ neurons regulate esophageal motility

The paper identifies and characterizes Prox2+ and Runx3+ vagal sensory neurons and shows their essential roles in esophageal peristalsis and swallowing.

High-resolution molecular atlas of a lung tumor in 3D

This paper presents a 3D spatial atlas of a human lung carcinoma, revealing tumor microenvironment niches and their associated immune interactions and survival outcomes.

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner

The paper shows that Cdr1as regulates miR-7 activity, which controls glutamatergic transmission and neuronal connectivity in forebrain neurons.

Rapid nuclear deadenylation of mammalian messenger RNA

The paper quantifies nuclear and cytoplasmic poly(A) tail dynamics, showing rapid nuclear deadenylation and distinct tail lengths for different transcripts.

Cell type diversity in a developing octopus brain

The paper profiles cell diversity in the paralarval octopus brain to create a cell type atlas and identifies molecular similarities between octopus and fly glial cells.

Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury

This study uses urinary single-cell RNA sequencing to analyze injury and repair processes in acute kidney injury, identifying distinct cellular and molecular dynamics.

Optocoder: computational decoding of spatially indexed bead arrays

Optocoder decodes spatially indexed bead arrays from microscopy images to match barcodes with sequenced data, improving accuracy and efficiency.

Spacemake: processing and analysis of large-scale spatial transcriptomics data

Spacemake processes and analyzes large-scale spatial transcriptomics data across different technologies, offering a modular and scalable pipeline with integration capabilities.

Transcriptomic responses of the human kidney to acute injury at single cell resolution

This study uses single-nuclei transcriptomics to analyze human kidney injury responses, identifying four injury-associated cell states and showing similar gene expression changes between AKI patients with and without COVID-19.

The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis

This study identifies IL-12 as the main driver of neuroinflammation in Alzheimer's disease by affecting oligodendrocyte survival and neuronal homeostasis in a mouse model.

Parallel genetics of regulatory sequences in vivo

The paper functionally analyzes regulatory sequences in C. elegans by introducing mutations and measuring their effects on gene expression and fitness.

SURF1 mutations causative of Leigh syndrome impair human neurogenesis

This study shows SURF1 mutations impair human neurogenesis by generating patient-derived iPS cells and demonstrating defects in neuronal differentiation and bioenergetics.

Neurodegeneration in human brain organoids infected with herpes simplex virus type 1

This study infects human brain organoids with HSV-1 and identifies molecular and cellular changes associated with neurodegeneration.

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

The paper uses bulk and single-cell transcriptomics to analyze SARS-CoV-2 infection in human cell lines, identifying HSP90 as a potential therapeutic target.