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Incorporating a series of analytical steps, from data extraction and quality control to the generation of low-dimensional representations and to longitudinal analyses, an open-source software is proposed to standardize current electronic health record data processing and analysis pipelines.
A single-cell transcriptomic study from the Human Cell Atlas integrating over 11 million brain cells from 70 studies uncovers differences across human brain regions and identifies rare progenitor and microglia subtypes.
SteatoSITE is an open resource that integrates histopathologic assessments, transcriptomic data and longitudinal electronic health records for a cohort of 940 patients with metabolic dysfunction-associated steatotic liver disease.
A single-cell atlas of the human lungs, integrating data from 2.4 million cells from 486 individuals and including samples from healthy and diseased lungs, provides a roadmap for the generation of organ-scale cell atlases.
A single-cell analysis of tumor-infiltrating T cells from 16 cancer types identifies new T cell subsets and a stress response cell state enriched in tumors resistant to immunotherapy.
A large, publicly available dataset integrating RNA, whole-exome, T cell receptor and 16S rRNA sequencing from patients with colon cancer enables the discovery of a prognostic score consisting of tumor, immune and microbial features.
A set of ready-to-use tools for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq facilitates the implementation of single-cell technologies in clinical settings and the construction of single-cell tumor atlases.
Large-scale, comprehensive proteomic profiling of Alzheimer’s disease brain and cerebrospinal fluid reveals disease-associated protein coexpression modules and highlights the importance of glia and energy metabolism in disease pathogenesis.
Genetically engineered mouse models representing the spectrum of human cutaneous melanoma provide a platform for studying clinical responses to immunotherapy.
A comprehensive biobank of bacterial isolates with longitudinal and multi-omics characterization will advance understanding of the diversity and functions of human gut bacteria.
Systematic metabolite profiling across cancer cell lines uncovers patterns associated with genetic and epigenetic features and reveals dysregulated metabolic states that can be exploited for anticancer therapy
A biobank of ovarian cancer organoids recapitulates the histopathological and molecular hallmarks of patient tumors and provides a resource for preclinical research.
An integrated analysis of glioma samples from patients with neurofibromatosis 1 annotates their mutational, epigenetic, transcriptional, and immunological features and uncovers similitudes with a subset of sporadic gliomas.
Personal ‘omics’ analysis of a single individual over a period of 3 years reveals that different types of omics data associate with episodes of acute and chronic disease.
A resource of preclinical pediatric brain tumor models with detailed molecular characterization provides a platform for the community to test novel therapeutic approaches.
A quantitative proteomic approach overcomes a major bottleneck in translational immunology, namely the identification of autologous and bacterial immunodominant major histocompatibility complex class II epitopes based on genomic sequences.
In-depth methylation analysis of formalin-fixed paraffin-embedded glioblastoma samples demonstrates heterogeneity between primary and recurring tumors and enables prediction of composition of the tumor microenvironment and insights into progression.
