Gabriele Gut
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View article: Histopathology-based protein multiplex generation using deep learning
Histopathology-based protein multiplex generation using deep learning Open
View article: Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma
Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma Open
View article: Pathology-oriented multiplexing enables integrative disease mapping
Pathology-oriented multiplexing enables integrative disease mapping Open
View article: Feasibility of multiomics tumor profiling for guiding treatment of melanoma
Feasibility of multiomics tumor profiling for guiding treatment of melanoma Open
There is limited evidence supporting the feasibility of using omics and functional technologies to inform treatment decisions. Here we present results from a cohort of 116 melanoma patients in the prospective, multicentric observational Tu…
View article: Precision Oncology Program (POP), an observational study using real-world data and imaging mass cytometry to explore decision support for the Molecular Tumor Board: study protocol
Precision Oncology Program (POP), an observational study using real-world data and imaging mass cytometry to explore decision support for the Molecular Tumor Board: study protocol Open
Introduction Precision oncology aims to provide individualised treatment recommendations based on patient-specific characteristics. In this rapidly evolving field with increasing numbers of biomarkers and potential therapeutic targets, the…
View article: AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery
AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery Open
Spatial proteomics technologies have transformed our understanding of complex tissue architectures by enabling simultaneous analysis of multiple molecular markers and their spatial organization. The high dimensionality of these data, varyi…
View article: Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia
Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia Open
View article: Learning Personalized Treatment Decisions in Precision Medicine: Disentangling Treatment Assignment Bias in Counterfactual Outcome Prediction and Biomarker Identification
Learning Personalized Treatment Decisions in Precision Medicine: Disentangling Treatment Assignment Bias in Counterfactual Outcome Prediction and Biomarker Identification Open
Precision medicine has the potential to tailor treatment decisions to individual patients using machine learning (ML) and artificial intelligence (AI), but it faces significant challenges due to complex biases in clinical observational dat…
View article: Probabilistic pathway-based multimodal factor analysis
Probabilistic pathway-based multimodal factor analysis Open
Motivation Multimodal profiling strategies promise to produce more informative insights into biomedical cohorts via the integration of the information each modality contributes. To perform this integration, however, the development of nove…
View article: Towards AI-Based Precision Oncology: A Machine Learning Framework for Personalized Counterfactual Treatment Suggestions based on Multi-Omics Data
Towards AI-Based Precision Oncology: A Machine Learning Framework for Personalized Counterfactual Treatment Suggestions based on Multi-Omics Data Open
AI-driven precision oncology has the transformative potential to reshape cancer treatment by leveraging the power of AI models to analyze the interaction between complex patient characteristics and their corresponding treatment outcomes. N…
View article: Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer
Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer Open
Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients pres…
View article: Author Correction: Learning single-cell perturbation responses using neural optimal transport
Author Correction: Learning single-cell perturbation responses using neural optimal transport Open
View article: Learning single-cell perturbation responses using neural optimal transport
Learning single-cell perturbation responses using neural optimal transport Open
Understanding and predicting molecular responses in single cells upon chemical, genetic or mechanical perturbations is a core question in biology. Obtaining single-cell measurements typically requires the cells to be destroyed. This makes …
View article: Multimodal spatiotemporal phenotyping of human retinal organoid development
Multimodal spatiotemporal phenotyping of human retinal organoid development Open
View article: Iterative Indirect Immunofluorescence Imaging (4i) on Adherent Cells and Tissue Sections
Iterative Indirect Immunofluorescence Imaging (4i) on Adherent Cells and Tissue Sections Open
Highly multiplexed protein measurements from multiple spatial scales using fluorescence microscopy recently emerged as a powerful way to investigate tumor microenvironments in biomedicine and the multivariate nature of complex systems' int…
View article: Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings
Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings Open
Comparing unpaired samples of a distribution or population taken at different points in time is a fundamental task in many application domains where measuring populations is destructive and cannot be done repeatedly on the same sample, suc…
View article: Learning Single-Cell Perturbation Responses using Neural Optimal Transport
Learning Single-Cell Perturbation Responses using Neural Optimal Transport Open
Understanding and predicting molecular responses in single cells upon chemical, genetic, or mechanical perturbations is a core question in biology. Obtaining single-cell measurements typically requires the cells to be destroyed. This makes…
View article: scROSHI: robust supervised hierarchical identification of single cells
scROSHI: robust supervised hierarchical identification of single cells Open
Identifying cell types based on expression profiles is a pillar of single cell analysis. Existing machine-learning methods identify predictive features from annotated training data, which are often not available in early-stage studies. Thi…
View article: Multimodal spatiotemporal phenotyping of human organoid development
Multimodal spatiotemporal phenotyping of human organoid development Open
Organoids generated from human pluripotent stem cells (PSCs) provide experimental systems to study development and disease. However, we lack quantitative spatiotemporal descriptions of organoid development that incorporate measurements acr…
View article: Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging
Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging Open
Advancing age causes reduced hippocampal neurogenesis, associated with age-related cognitive decline. The spatial relationship of age-induced alterations in neural stem cells (NSCs) and surrounding cells within the hippocampal niche remain…
View article: Learning Single-Cell Perturbation Responses using Neural Optimal Transport
Learning Single-Cell Perturbation Responses using Neural Optimal Transport Open
The ability to understand and predict molecular responses towards external perturbations is a core question in molecular biology. Technological advancements in the recent past have enabled the generation of high-resolution single-cell data…
View article: Author response: Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging
Author response: Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging Open
View article: Establishing standardized immune phenotyping of metastatic melanoma by digital pathology
Establishing standardized immune phenotyping of metastatic melanoma by digital pathology Open
View article: Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging
Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging Open
Advancing age causes reduced hippocampal neurogenesis, associated with age-related cognitive decline. The spatial relationship of age-induced alterations in neural stem cells (NSCs) and surrounding cells within the hippocampal niche remain…
View article: The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support
The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support Open
View article: SCIM: universal single-cell matching with unpaired feature sets
SCIM: universal single-cell matching with unpaired feature sets Open
Motivation Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clin…
View article: The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support
The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support Open
Recent technological advances allow profiling of tumor samples to an unparalleled level with respect to molecular and spatial composition as well as treatment response. We describe a prospective, observational clinical study performed with…
View article: Trajectories of cell-cycle progression from fixed cell populations
Trajectories of cell-cycle progression from fixed cell populations Open