Nico Kaiser

Integrative omics and phase IIa clinical trial identify TNF as key node in autoimmune hepatitis

Yang Xu, Jan Philipp Weltzsch, Christoph Kilian, Babett Steglich et autres

BACKGROUND & AIMS: Patients with autoimmune hepatitis (AIH) experience increased mortality and severe side effects from non-specific immunosuppressive therapy, highlighting an urgent need for targeted treatment approaches. Here, we aimed to delineate the cellular and molecular network underlying AIH within its spatial …

de, cl, dk (code pays fourni par la source)

SCALE: unsupervised multiscale domain identification in spatial omics data

Behnam Yousefi, Darius P. Schaub, R Khatri, Nico Kaiser et autres

Single-cell spatial transcriptomics enables precise mapping of cellular states and functional domains within their native tissue environment. These functional domains often exist at multiple spatial scales, with larger domains encompassing smaller ones, reflecting the hierarchical organization of biological systems. However, the identification …

de, dk (code pays fourni par la source)

A systematic analysis of the impact of data variation on AI-based histopathological grading of prostate cancer

Patrick Fuhlert, Fabian Westhaeusser, Esther Dietrich, Maximilian Lennartz et autres

The histopathological evaluation of biopsies by human experts is a gold standard in clinical disease diagnosis. While recent artificial intelligence-based (AI) approaches have reached human expert-level performance, they often display shortcomings caused by variations in sample preparation, limiting clinical applicability. This study …

de, se, gb, dk (code pays fourni par la source)

BioContextAI is a community hub for agentic biomedical systems

Malte Kuehl, Darius P. Schaub, Francesco Carli, Lukas Heumos et autres

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

Metabolite-enhanced normothermic machine perfusion improves kidney transplant viability

Jan Czogalla, Fabian Hausmann, Simon Lagies, Sydney E. Gies et autres

Normothermic machine perfusion (NMP) has become a valuable tool to expand the pool of transplantable organs. However, the application of NMP to kidneys presents substantial challenges, mostly due to high variability in the composition of currently used perfusion solutions. Here, we provide …

de, us, jp, it, nl, dk (code pays fourni par la source)

Community-based biomedical context to unlock agentic systems

Malte Kuehl, Darius P. Schaub, Francesco Carli, Lukas Heumos et autres

Large language models (LLMs) face reliability challenges stemming from hallucinations and insufficient access to validated scientific resources. Existing solutions are often fragmented and limited to specific applications, hindering broader adoption and interoperability. Here, we present Biomedical Context for Artificial Intelligence (BioContextAI), an …

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

Pathology-oriented multiplexing enables integrative disease mapping

Malte Kuehl, Yusuke Okabayashi, Milagros N. Wong, Lukas Gernhold et autres

, the integration of biological layers (that is, cell structure, subcellular domains and signalling activity) remains challenging. This is due to limitations in the compositions of antibody panels and image resolution, which together restrict the scope of image analysis. Here we present …

de, dk, jp, ch, au, fr, us (code pays fourni par la source)

SCALE: Unsupervised Multi-Scale Domain Identification in Spatial Omics Data

Behnam Yousefi, Darius P. Schaub, Robin Khatri, Nico Kaiser et autres

Single-cell spatial transcriptomics enables precise mapping of cellular states and functional domains within their native tissue environment. These functional domains often exist at multiple spatial scales, with larger domains encompassing smaller ones, reflecting the hierarchical organization of biological systems. However, the identification …

de, dk (code pays fourni par la source)

THU-311-YI Uncovering novel therapeutic targets for autoimmune hepatitis (AIH): detection via omics integration and validation in proof-of- concept clinical trial

Yang Xu, Jan Philipp Weltzsch, Christoph Kilian, Babett Steglich et autres

New treatment targets in autoimmune hepatitis: detection using integrative omics and target validation in a proof of concept phase II clinical trial

Jan Philipp Weltzsch, Yang Xu, Christoph Kilian, Babett Steglich et autres

Standard immunosuppression for autoimmune hepatitis (AIH) is non-specific with corticosteroids as drug of choice for remission induction. An improved understanding of the underlying pathophysiology is needed and could enable a tailored therapeutic approach and avoid side effects associated with standard therapy. We …

de, cl (code pays fourni par la source)

PCA-based spatial domain identification with state-of-the-art performance

Darius P. Schaub, Behnam Yousefi, Nico Kaiser, Robin Khatri et autres

MOTIVATION: The identification of biologically meaningful domains is a central step in the analysis of spatial transcriptomic data. RESULTS: Following Occam's razor, we show that a simple PCA-based algorithm for unsupervised spatial domain identification rivals the performance of ten competing state-of-the-art methods …

de, dk (code pays fourni par la source)

PCA-based spatial domain identification with state-of-the-art performance

Darius P. Schaub, Behnam Yousefi, Nico Kaiser, Robin Khatri et autres

The identification of biologically meaningful domains is a central step in the analysis of spatial transcriptomic data. Following Occam's razor, we show that a simple PCA-based algorithm for spatial domain identification rivals the performance of ten competing state-of-the-art methods across six single-cell …

de, dk (code pays fourni par la source)